Generated 2026-05-12. Project: ~/conserved_site_project/
System
| Component |
Version |
Source |
| macOS |
Darwin 25.4.0 (arm64) |
system |
| Python |
3.11.9 |
pyenv |
| Homebrew |
latest |
system |
Native binaries (Homebrew)
| Tool |
Version |
Formula |
| AutoDock Vina |
AutoDock Vina v1.2.7 |
brewsci/bio/autodock-vina |
| PyMOL |
3.1.0_3 (headless render OK) |
homebrew/core/pymol |
| MAFFT |
v7.526 (2024/Apr/26) |
homebrew/core/mafft |
| OpenBabel (CLI) |
Open Babel 3.1.0 – May 8 2020 – 15:48:11 |
homebrew/core/open-babel |
| Boost C++ libs |
1.85.0_3 (vina dep) |
brewsci/bio/boost@1.85 |
| GLEW |
2.3.1 (pymol GL dep) |
homebrew/core/glew |
| libxml2 |
system + homebrew/core/libxml2 |
homebrew/core/libxml2 |
Python venv (.venv, Python 3.11.9)
Selected scientific packages (full freeze in pip_freeze.txt).
| Package |
Version |
Used for |
| biopython |
1.87 |
MSA parsing, PDB I/O, FASTA |
| rdkit |
2026.3.1 |
ligand handling, charge fallback |
| prody |
2.6.1 |
structure analysis (loaded as sanity check) |
| MDAnalysis |
2.10.0 |
trajectory libs (kept for future MD extension) |
| meeko |
0.7.1 |
AutoDock Vina prep helpers (mk_prepare_*) |
| gemmi |
0.7.5 |
structural file I/O (meeko dep) |
| pyfamsa |
0.7.0 |
MSA fallback (unused; MAFFT used) |
| matplotlib |
3.10.9 |
figures |
| matplotlib-venn |
1.1.2 |
Stage 2 overlap diagram |
| seaborn |
0.13.2 |
heatmap, scatter |
| pandas |
3.0.3 |
results tables |
| numpy |
2.4.4 |
JSD + numerics |
| scipy |
1.17.1 |
stats helpers |
| requests |
2.34.0 |
UniProt / PDBe REST |
| jinja2 |
3.1.6 |
report templating |
| weasyprint |
68.1 |
HTML→PDF |
| python-docx |
1.2.0 |
HTML→DOCX (final report) |
| openbabel-wheel |
3.1.1.23 |
Python OpenBabel bindings (CLI used) |
| Attempted |
Failure mode |
Workaround used |
vina Python pkg (pip) |
Build failed: missing Boost headers in pip wheel |
Used Vina CLI v1.2.7 via subprocess |
pymol-open-source (pip) |
Wheel hardcoded paths from another user’s mamba env (libGLEW.2.1, libxml2 from /Users/Martin/) |
Used Homebrew PyMOL 3.1.0 binary headless via subprocess |
| Modeller / Rosetta |
Not installed (heavy, license) |
PyMOL Mutagenesis Wizard rotamer pick (acknowledged caveat) |